Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 92 of 318
Found at i:30773147 original size:24 final size:24
Alignment explanation
Indices: 30773118--30773172 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
30773108 TAAAAATATA
30773118 AAATTTTTATTTAAA-TT-TATTTAT
1 AAATTTTTA--TAAATTTATATTTAT
30773142 AAA-TTTTATAAATTTTATATTTAT
1 AAATTTTTATAAA-TTTATATTTAT
30773166 AAATTTT
1 AAATTTT
30773173 ACAAGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 4 0.15
23 7 0.26
24 13 0.48
25 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
AAATTTTTATAAATTTATATTTAT
Found at i:30773151 original size:9 final size:9
Alignment explanation
Indices: 30773137--30773173 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
30773127 TTTAAATTTA
30773137 TTTATAAAT
1 TTTATAAAT
30773146 TTTATAAAT
1 TTTATAAAT
30773155 TTTAT--A-
1 TTTATAAAT
30773161 TTTATAAAT
1 TTTATAAAT
30773170 TTTA
1 TTTA
30773174 CAAGATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 5 0.20
7 1 0.04
8 1 0.04
9 18 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTATAAAT
Found at i:30773173 original size:24 final size:25
Alignment explanation
Indices: 30773135--30773182 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
30773125 TATTTAAATT
*
30773135 TATTTATAAATTTTATAA-ATTTTA
1 TATTTATAAATTTTACAAGATTTTA
30773159 TATTTATAAATTTTACAAGATTTT
1 TATTTATAAATTTTACAAGATTTT
30773183 CAATAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
TATTTATAAATTTTACAAGATTTTA
Found at i:30773425 original size:15 final size:15
Alignment explanation
Indices: 30773407--30773453 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
30773397 TTTTTAAAGA
30773407 TTATATTTTAGTTAT
1 TTATATTTTAGTTAT
* **
30773422 TTATATTTAAAAT-T
1 TTATATTTTAGTTAT
*
30773436 TTATATTTTAGTCAT
1 TTATATTTTAGTTAT
30773451 TTA
1 TTA
30773454 CGTTATAGTT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (15 bp):
TTATATTTTAGTTAT
Found at i:30775182 original size:111 final size:115
Alignment explanation
Indices: 30774972--30775234 Score: 336
Period size: 112 Copynumber: 2.3 Consensus size: 115
30774962 CTAGTAATTT
* * * *
30774972 TTTTTTGTTCTGGCCTTATAATGGCCGGCACTAAGGACTTTTATCATGTTCCAATGCAATTTTTT
1 TTTTTGGTTCTGGCCTTCTAATGGCCGGCACCAAGGACTTTTATCATGTCCCAATGCAATTTTTT
30775037 ATTTTAATTTTCTACACTGATGGCCAACACCAGACTAGT-AAAAAA-AAA
66 ATTTTAATTTTCTACACTGATGGCCAACACCAGACTAGTAAAAAAAGAAA
* * * * **
30775085 -TTTTGGTTCTGGCCTTCTAATGGCCGACACCAGGGGCTTTTTTTGTGTCCCAATGCAATTTTTT
1 TTTTTGGTTCTGGCCTTCTAATGGCCGGCACCAAGGACTTTTATCATGTCCCAATGCAATTTTTT
* * ** *
30775149 -TTTTACTTTTCTACATTGATGGCCGGCACCAGACTTGTAAAAAAAGAAA
66 ATTTTAATTTTCTACACTGATGGCCAACACCAGACTAGTAAAAAAAGAAA
30775198 TTTTTTTGGGTTCTGGCCTTCTAATGGCCGGCACCAA
1 --TTTTT-GGTTCTGGCCTTCTAATGGCCGGCACCAA
30775235 ATTTATCATC
Statistics
Matches: 127, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
111 33 0.26
112 60 0.47
113 3 0.02
116 4 0.03
117 27 0.21
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (115 bp):
TTTTTGGTTCTGGCCTTCTAATGGCCGGCACCAAGGACTTTTATCATGTCCCAATGCAATTTTTT
ATTTTAATTTTCTACACTGATGGCCAACACCAGACTAGTAAAAAAAGAAA
Found at i:30778079 original size:28 final size:27
Alignment explanation
Indices: 30777978--30778079 Score: 71
Period size: 28 Copynumber: 3.5 Consensus size: 27
30777968 TCAGTGTTAA
* *
30777978 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
30778006 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
* *
30778038 ATTGGACCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
30778066 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
30778080 TATTACAAGT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
27 6 0.11
28 27 0.47
30 2 0.04
32 16 0.28
33 6 0.11
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:30778099 original size:60 final size:59
Alignment explanation
Indices: 30777986--30778115 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 59
30777976 AACTGGGCCT
* *
30777986 TAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTATATTGGACC
1 TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAG-ATCAGAGTATATTGGACC
* * *
30778046 TAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATATATTGGGCC
1 TAGCCCATATCAATATCAATCTGGGCCATAGCCC-ATTACAGA-TCAGAG-TATATTGGACC
*
30778106 TTGCCCATAT
1 TAGCCCATAT
30778116 TAACACAGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
59 4 0.07
60 52 0.85
61 5 0.08
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (59 bp):
TAGCCCATATCAATATCAATCTGGGCCATAGCCCATTACAGATCAGAGTATATTGGACC
Found at i:30782985 original size:60 final size:60
Alignment explanation
Indices: 30782907--30783043 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
30782897 CAGTGTTAAC
* *
30782907 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCC-CTTAC-AGTATC-AGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAG--TCGAGA-TATAT
* *
30782968 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
*
30783028 TGGGCCTTGCCCATAT
1 TGGGCCTAGCCCATAT
30783044 TAACACAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
60 53 0.78
61 13 0.19
62 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (60 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTCGAGATATAT
Found at i:30783007 original size:28 final size:27
Alignment explanation
Indices: 30782906--30783007 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 27
30782896 TCAGTGTTAA
* *
30782906 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCC-TAGCCCATATCAGTATCAAT
*
30782934 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCC-TAGCCCATAT-CAGTATC--A--AT
*
30782966 ATTGGGCCTAGCCCATATCAGTATCAAT
1 -CTGGGCCTAGCCCATATCAGTATCAAT
30782994 CTGGGCCGTAGCCC
1 CTGGGCC-TAGCCC
30783008 TATTACAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
27 7 0.12
28 27 0.46
30 2 0.03
32 16 0.27
33 7 0.12
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (27 bp):
CTGGGCCTAGCCCATATCAGTATCAAT
Found at i:30784655 original size:21 final size:21
Alignment explanation
Indices: 30784629--30784677 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
30784619 AATGGAAAAA
30784629 CGTGGTTCTAAGTAGATATAC
1 CGTGGTTCTAAGTAGATATAC
30784650 CGTGGTTCTAAGTAGATATAC
1 CGTGGTTCTAAGTAGATATAC
*
30784671 CATGGTT
1 CGTGGTT
30784678 ATACGTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (21 bp):
CGTGGTTCTAAGTAGATATAC
Found at i:30784807 original size:47 final size:47
Alignment explanation
Indices: 30784685--30784896 Score: 244
Period size: 47 Copynumber: 4.7 Consensus size: 47
30784675 GTTATACGTG
* * * *
30784685 TAACGCGGTGCTAAGTGGATATACCACGATTACACATATTGATGCAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
*
30784732 GTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCAT
1 -TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* *
30784780 TAACGTGGTGCTAAGTGGATATACCACGATTA-A-ACA-TG------
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* * * *
30784818 TAACATGGTGCTAAGTAGATATGCCACGGTTACATATATTGATTTAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
*
30784865 TAACGTGGTGCTAAGTGGATATACCACAGTTA
1 TAACGTGGTGCTAAGTGGATATACCACGGTTA
30784897 AACATGTAAC
Statistics
Matches: 138, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
38 28 0.20
39 1 0.01
40 2 0.01
41 2 0.01
44 2 0.01
45 2 0.01
46 1 0.01
47 58 0.42
48 42 0.30
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (47 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
Found at i:30784830 original size:85 final size:85
Alignment explanation
Indices: 30784729--30784934 Score: 360
Period size: 85 Copynumber: 2.4 Consensus size: 85
30784719 CATATTGATG
*
30784729 CATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAA
1 CATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAA
30784794 GTGGATATACCAC-GATTAAA
66 GTGGATATACCACAG-TTAAA
* *
30784814 CATGTAACATGGTGCTAAGTAGATATGCCACGGTTACATATATTGATTTATTAACGTGGTGCTAA
1 CATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAA
30784879 GTGGATATACCACAGTTAAA
66 GTGGATATACCACAGTTAAA
*
30784899 CATGTAACATGGTGCTAAGTGGATATGCCACAGTTA
1 CATGTAACATGGTGCTAAGTGGATATGCCACGGTTA
30784935 TACATGTTAA
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 114 0.99
86 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (85 bp):
CATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTAA
GTGGATATACCACAGTTAAA
Found at i:30784839 original size:38 final size:38
Alignment explanation
Indices: 30784780--30784929 Score: 140
Period size: 38 Copynumber: 3.7 Consensus size: 38
30784770 ATTGATTCAT
*
30784780 TAACGTGGTGCTAAGTGGATATACCACGATTAAACATG
1 TAACATGGTGCTAAGTGGATATACCACGATTAAACATG
* * * *
30784818 TAACATGGTGCTAAGTAGATATGCCACGGTTACATATATTG
1 TAACATGGTGCTAAGTGGATATACCACGATTA-A-ACA-TG
*
30784859 ATTTATTAACGTGGTGCTAAGTGGATATACCAC-AGTTAAACATG
1 ------TAACATGGTGCTAAGTGGATATACCACGA-TTAAACATG
*
30784903 TAACATGGTGCTAAGTGGATATGCCAC
1 TAACATGGTGCTAAGTGGATATACCAC
30784930 AGTTATACAT
Statistics
Matches: 90, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
38 53 0.59
39 1 0.01
40 2 0.02
41 2 0.02
44 2 0.02
45 2 0.02
46 1 0.01
47 27 0.30
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (38 bp):
TAACATGGTGCTAAGTGGATATACCACGATTAAACATG
Found at i:30784930 original size:38 final size:38
Alignment explanation
Indices: 30784865--30784941 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
30784855 ATTGATTTAT
*
30784865 TAACGTGGTGCTAAGTGGATATACCACAGTTAAACATG
1 TAACATGGTGCTAAGTGGATATACCACAGTTAAACATG
* *
30784903 TAACATGGTGCTAAGTGGATATGCCACAGTTATACATG
1 TAACATGGTGCTAAGTGGATATACCACAGTTAAACATG
30784941 T
1 T
30784942 TAATTTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (38 bp):
TAACATGGTGCTAAGTGGATATACCACAGTTAAACATG
Found at i:30787471 original size:76 final size:76
Alignment explanation
Indices: 30787314--30787584 Score: 359
Period size: 76 Copynumber: 3.6 Consensus size: 76
30787304 AATTTACAAG
30787314 GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTTCAAAGAAATGGGAAAAAAACT
1 GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTTCAAAGAAATGGGAAAAAAA-T
30787379 AAAATTAAAATT
65 AAAATTAAAATT
** *
30787391 GAAAGAAAGATAAATTTAAACAAAATAAGGAAAAAATTTAATTTCAAAGAAATGGGAAAAAATTA
1 GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTTCAAAGAAATGGGAAAAAAATA
30787456 AAATTAAAATT
66 AAATTAAAATT
** * * *
30787467 GAAAGAAAGATAAATTTAAATGAAATGGGGAAAAATTTTAATTT-AAATTAAATGAGAAAAAAAT
1 GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTTCAAA-GAAATGGGAAAAAAAT
*** *
30787531 -AAATTTGCATG
65 AAAATTAAAATT
* * * *
30787542 GAAAGATAGAT-AATTTAAATGAAATGAGAAAAAAATTAAATTT
1 GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTT
30787585 GTATGGAAAA
Statistics
Matches: 173, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
74 28 0.16
75 20 0.12
76 65 0.38
77 60 0.35
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (76 bp):
GAAAGAAAGATAAATTTAAATGAAATAAGGAAAAAATTTAATTTCAAAGAAATGGGAAAAAAATA
AAATTAAAATT
Found at i:30787580 original size:21 final size:21
Alignment explanation
Indices: 30787556--30787678 Score: 63
Period size: 21 Copynumber: 5.5 Consensus size: 21
30787546 GATAGATAAT
30787556 TTAAATGAAATGAGAAAAAAA
1 TTAAATGAAATGAGAAAAAAA
* *
30787577 TTAAATTTG-TATGGAAAAATAGATAA
1 TTAAA--TGAAAT-GAGAAA-A-A-AA
* **
30787603 TTTAAATGAAATGAGGAAAATT
1 -TTAAATGAAATGAGAAAAAAA
* *
30787625 TTAATTTAAAT-A-AAAAATAA
1 TTAAATGAAATGAGAAAAA-AA
30787645 TATAAATGAAATGAGAAAAAAAA
1 T-TAAATGAAATGAG-AAAAAAA
30787668 TTAAATTGAAA
1 TTAAA-TGAAA
30787679 AAAATATAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 26
0.65 0.12 0.23
Matches are distributed among these distances:
19 4 0.05
20 2 0.03
21 22 0.30
22 7 0.09
23 16 0.22
24 7 0.09
25 7 0.09
26 4 0.05
27 5 0.07
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (21 bp):
TTAAATGAAATGAGAAAAAAA
Found at i:30787583 original size:27 final size:27
Alignment explanation
Indices: 30787324--30787584 Score: 103
Period size: 27 Copynumber: 10.3 Consensus size: 27
30787314 GAAAGAAAGA
* *
30787324 TAAATTTAAATGAAATAAGGAAAAAAT
1 TAAATTTAAATGAAATGAGAAAAAAAT
* * *
30787351 TTAATTTCAAA-GAAATGGGAAAAAAAC
1 TAAATTT-AAATGAAATGAGAAAAAAAT
* * *
30787378 TAAAATT-AA--AATTGA-AAGAAAGA-
1 TAAATTTAAATGAAATGAGAA-AAAAAT
** * *
30787401 TAAATTTAAACAAAATAAGGAAAAAAT
1 TAAATTTAAATGAAATGAGAAAAAAAT
* *
30787428 TTAATTTCAAA-GAAATG-GGAAAAAAT
1 TAAATTT-AAATGAAATGAGAAAAAAAT
* * *
30787454 TAAAATT-AA--AATTGA-AAGAAAGA-
1 TAAATTTAAATGAAATGAGAA-AAAAAT
* * *
30787477 TAAATTTAAATGAAATGGGGAAAAATT
1 TAAATTTAAATGAAATGAGAAAAAAAT
* *
30787504 TTAATTTAAATTAAATGAGAAAAAAA-
1 TAAATTTAAATGAAATGAGAAAAAAAT
** * * *
30787530 TAAATTTGCATGGAA--AG--ATAGA-
1 TAAATTTAAATGAAATGAGAAAAAAAT
30787552 T-AATTTAAATGAAATGAGAAAAAAAT
1 TAAATTTAAATGAAATGAGAAAAAAAT
30787578 TAAATTT
1 TAAATTT
30787585 GTATGGAAAA
Statistics
Matches: 167, Mismatches: 46, Indels: 42
0.65 0.18 0.16
Matches are distributed among these distances:
21 10 0.06
22 4 0.02
23 21 0.13
24 20 0.12
25 5 0.03
26 40 0.24
27 61 0.37
28 6 0.04
ACGTcount: A:0.59, C:0.02, G:0.13, T:0.26
Consensus pattern (27 bp):
TAAATTTAAATGAAATGAGAAAAAAAT
Found at i:30787599 original size:48 final size:48
Alignment explanation
Indices: 30787505--30787704 Score: 203
Period size: 48 Copynumber: 4.4 Consensus size: 48
30787495 GGAAAAATTT
* * *
30787505 TAATTTAAATTAAATGAGAAAAAAA-TAAATTTGCATGGAAAGATAGA
1 TAATTTAAATGAAATGAGAAAAAAATTAAATTTGAATGGAAAAATAGA
*
30787552 TAATTTAAATGAAATGAGAAAAAAATTAAATTTGTATGGAAAAATAGA
1 TAATTTAAATGAAATGAGAAAAAAATTAAATTTGAATGGAAAAATAGA
* * * *
30787600 TAATTTAAATGAAATGAG-GAAAATTTTAATTTAAAT---AAAA-A-A
1 TAATTTAAATGAAATGAGAAAAAAATTAAATTTGAATGGAAAAATAGA
*
30787642 TAATATAAATGAAATGAGAAAAAAAATTAAA-TTGAA---AAAAAT--A
1 TAATTTAAATGAAATGAG-AAAAAAATTAAATTTGAATGGAAAAATAGA
*
30787685 TAGTTTAAATGAAATG-GAAA
1 TAATTTAAATGAAATGAGAAA
30787705 TGAAATGAAA
Statistics
Matches: 133, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
41 3 0.02
42 19 0.14
43 24 0.18
44 12 0.09
47 37 0.28
48 38 0.29
ACGTcount: A:0.58, C:0.01, G:0.13, T:0.28
Consensus pattern (48 bp):
TAATTTAAATGAAATGAGAAAAAAATTAAATTTGAATGGAAAAATAGA
Found at i:30787607 original size:27 final size:27
Alignment explanation
Indices: 30787530--30787609 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
30787520 GAGAAAAAAA
* *
30787530 TAAATTTGCATGGAAAGATAGATAATT
1 TAAATTTGAATGGAAAAATAGATAATT
*
30787557 TAAA--TGAAAT-GAGAAA-A-A-AA-T
1 TAAATTTG-AATGGAAAAATAGATAATT
*
30787578 TAAATTTGTATGGAAAAATAGATAATT
1 TAAATTTGAATGGAAAAATAGATAATT
30787605 TAAAT
1 TAAAT
30787610 GAAATGAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
21 5 0.12
22 4 0.10
23 8 0.20
24 2 0.05
25 7 0.17
26 4 0.10
27 10 0.25
ACGTcount: A:0.53, C:0.01, G:0.15, T:0.31
Consensus pattern (27 bp):
TAAATTTGAATGGAAAAATAGATAATT
Found at i:30787709 original size:5 final size:5
Alignment explanation
Indices: 30787691--30787720 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
30787681 AATATAGTTT
30787691 AAATG AAATGG AAATG AAATG AAATG AAAT
1 AAATG AAAT-G AAATG AAATG AAATG AAAT
30787721 TTGAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
AAATG
Found at i:30787710 original size:16 final size:15
Alignment explanation
Indices: 30787691--30787720 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30787681 AATATAGTTT
30787691 AAATGAAATGGAAATG
1 AAATGAAAT-GAAATG
30787707 AAATGAAATGAAAT
1 AAATGAAATGAAAT
30787721 TTGAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
AAATGAAATGAAATG
Found at i:30788108 original size:5 final size:5
Alignment explanation
Indices: 30788098--30788198 Score: 60
Period size: 5 Copynumber: 18.0 Consensus size: 5
30788088 GAAAAAAATT
* *
30788098 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGA AATGTA ATTTA
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A AATGA
*
30788149 TAATGA ATATGA AATTA AATGA AATGTTA AATGA ACAT-A ATATGA AATGA
1 -AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA A-ATGA AATGA
30788199 TGATTATGAA
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
5 40 0.51
6 25 0.32
7 13 0.17
ACGTcount: A:0.53, C:0.01, G:0.15, T:0.31
Consensus pattern (5 bp):
AATGA
Found at i:30788116 original size:30 final size:30
Alignment explanation
Indices: 30788078--30788198 Score: 96
Period size: 30 Copynumber: 4.0 Consensus size: 30
30788068 GAAAAGTAAT
30788078 AAAT-TTAAATGAAA-A-AAATTAATGAAATG
1 AAATGTTAAATGAAATATAAA-T-ATGAAATG
*
30788107 AAATGTTAAATGAAATATGAATATGAAATG
1 AAATGTTAAATGAAATATAAATATGAAATG
30788137 AAATGTAATTTATAATG-AATATGAAAT-T-AAATG
1 AAATG----TTA-AATGAAATAT-AAATATGAAATG
*
30788170 AAATGTTAAATG-AACAT-AATATGAAATG
1 AAATGTTAAATGAAATATAAATATGAAATG
30788198 A
1 A
30788199 TGATTATGAA
Statistics
Matches: 78, Mismatches: 3, Indels: 23
0.75 0.03 0.22
Matches are distributed among these distances:
26 3 0.04
27 1 0.01
28 14 0.18
29 7 0.09
30 23 0.29
31 2 0.03
32 2 0.03
33 10 0.13
34 9 0.12
35 7 0.09
ACGTcount: A:0.55, C:0.01, G:0.13, T:0.31
Consensus pattern (30 bp):
AAATGTTAAATGAAATATAAATATGAAATG
Found at i:30788119 original size:12 final size:12
Alignment explanation
Indices: 30788102--30788183 Score: 62
Period size: 12 Copynumber: 6.6 Consensus size: 12
30788092 AAAATTAATG
30788102 AAATGAAATGTT
1 AAATGAAATGTT
* *
30788114 AAATGAAATATG
1 AAATGAAATGTT
30788126 AATATGAAATG--
1 AA-ATGAAATGTT
*
30788137 AAATGTAAT-TT
1 AAATGAAATGTT
30788148 ATAATGAATATGAAATT
1 A-AATGAA-ATG---TT
30788165 AAATGAAATGTT
1 AAATGAAATGTT
30788177 AAATGAA
1 AAATGAA
30788184 CATAATATGA
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
10 6 0.11
11 3 0.05
12 26 0.46
13 9 0.16
15 3 0.05
16 6 0.11
17 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.32
Consensus pattern (12 bp):
AAATGAAATGTT
Found at i:30788120 original size:17 final size:16
Alignment explanation
Indices: 30788078--30788174 Score: 78
Period size: 17 Copynumber: 6.0 Consensus size: 16
30788068 GAAAAGTAAT
30788078 AAATTTAAATGAAA--
1 AAATTTAAATGAAATG
*
30788092 AAAATT-AATGAAATG
1 AAATTTAAATGAAATG
30788107 AAATGTTAAATGAAAT-
1 AAAT-TTAAATGAAATG
*
30788123 ATGAATATGAAATGAAATG
1 A--AAT-TTAAATGAAATG
*
30788142 TAATTTATAATGAATATG
1 AAATTTA-AATGAA-ATG
30788160 AAA-TTAAATGAAATG
1 AAATTTAAATGAAATG
30788175 TTAAATGAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 17
0.74 0.08 0.19
Matches are distributed among these distances:
13 7 0.10
14 5 0.07
15 6 0.09
16 11 0.16
17 20 0.30
18 18 0.27
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (16 bp):
AAATTTAAATGAAATG
Found at i:30788163 original size:28 final size:27
Alignment explanation
Indices: 30788099--30788197 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 27
30788089 AAAAAAATTA
**
30788099 ATGAAATGAAATGTTAAATGAAATATGAAT
1 ATGAAATGAAATG-T-AATTTAA-ATGAAT
30788129 ATGAAATGAAATGTAATTTATAATGAAT
1 ATGAAATGAAATGTAATTTA-AATGAAT
* * *
30788157 ATGAAATTAAATGAAATGTTAAATGAAC
1 ATGAAATGAAATGTAAT-TTAAATGAAT
30788185 AT-AATATGAAATG
1 ATGAA-ATGAAATG
30788198 ATGATTATGA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 5 0.08
30 13 0.22
ACGTcount: A:0.53, C:0.01, G:0.15, T:0.31
Consensus pattern (27 bp):
ATGAAATGAAATGTAATTTAAATGAAT
Found at i:30788342 original size:17 final size:18
Alignment explanation
Indices: 30788310--30788346 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
30788300 AAATGGAAAG
*
30788310 ATAGATAATTTAAATGAA
1 ATAGATAATGTAAATGAA
30788328 ATAGA-AATGTAAATGAA
1 ATAGATAATGTAAATGAA
30788345 AT
1 AT
30788347 GCAAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.30
Consensus pattern (18 bp):
ATAGATAATGTAAATGAA
Found at i:30790406 original size:47 final size:47
Alignment explanation
Indices: 30790344--30790469 Score: 155
Period size: 47 Copynumber: 2.7 Consensus size: 47
30790334 CTTTACATAA
* * * *
30790344 TGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCTCAC
1 TGATGCCATATCCCAGATATGGTCTTACACAGT-AGCACATATCACAC
* * *
30790391 TGATGTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
* *
30790438 CGATGCCATATCCCAGATATGGTCTTATACAG
1 TGATGCCATATCCCAGATATGGTCTTACACAG
30790470 AAATCACTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 67 0.97
48 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (47 bp):
TGATGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
Found at i:30790528 original size:31 final size:31
Alignment explanation
Indices: 30790493--30790701 Score: 274
Period size: 31 Copynumber: 6.7 Consensus size: 31
30790483 CTTGTCACTT
* *
30790493 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
30790524 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
30790555 GTAGTCGGAGCTGCCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
30790586 GTAGCTGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
30790617 GTAGCAGAAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
30790648 GTAGCTGAAACTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
30790679 GTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
30790702 GTTGTCATTT
Statistics
Matches: 155, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 155 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:30790799 original size:50 final size:49
Alignment explanation
Indices: 30790679--30790855 Score: 212
Period size: 50 Copynumber: 3.5 Consensus size: 49
30790669 CACTGATCAG
* * * * *
30790679 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGATAAGT
1 GTAGC-GAAGCTATCACTTATCACTT-TCACTTGTCC-TTAATCAGATAAGT
30790730 GTAGCTGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGC-GAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
* * * *
30790780 GTAGACGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAG-CGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
30790830 GTAGCCGAAGCTATCACTTATCACTT
1 GTAG-CGAAGCTATCACTTATCACTT
30790856 GTTTCCATGG
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
50 86 0.77
51 26 0.23
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (49 bp):
GTAGCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
Found at i:30794317 original size:85 final size:85
Alignment explanation
Indices: 30794202--30794441 Score: 238
Period size: 90 Copynumber: 2.7 Consensus size: 85
30794192 AGAAATTGAC
*
30794202 AAATTAAATTTACAGACACAATAAAATACAAACATTCTAAAATATTAATACA-AAAAA-TAAAAT
1 AAATTAAATTTA-AAACACAA-AAAATACAAACATTCTAAAA-ATTAATACACAAAAATTAAAAT
30794265 TCAAAC-A-AAAATAATACGCACT
63 TCAAACTACAAAA-AATACGCACT
* * *
30794287 AAATTAAATTTAAACACCCAAAAAACTACAAACATATGGGT-AAAATTAATACACAAAAATTTTA
1 AAATTAAATTTAAA-ACACAAAAAA-TACAAACAT-T--CTAAAAATTAATACACAAAAA-TTAA
* * *
30794351 AATTCAAACTACATAAAATATGGACT
60 AATTCAAACTACAAAAAATACGCACT
* *
30794377 AAATTAAATTTACAAATACAGAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAA
1 AAATTAAATTTA-AAACACA-AAAAATACAAACATTCTAA-AAATTAATACACAAAAAT-TAAAA
30794442 AATTAATCCT
Statistics
Matches: 128, Mismatches: 12, Indels: 26
0.77 0.07 0.16
Matches are distributed among these distances:
84 5 0.04
85 26 0.20
86 10 0.08
87 9 0.07
88 3 0.02
89 32 0.25
90 33 0.26
91 10 0.08
ACGTcount: A:0.58, C:0.13, G:0.04, T:0.24
Consensus pattern (85 bp):
AAATTAAATTTAAAACACAAAAAATACAAACATTCTAAAAATTAATACACAAAAATTAAAATTCA
AACTACAAAAAATACGCACT
Found at i:30794435 original size:89 final size:85
Alignment explanation
Indices: 30794202--30794441 Score: 247
Period size: 89 Copynumber: 2.7 Consensus size: 85
30794192 AGAAATTGAC
*
30794202 AAATTAAATTTACAGACACAATAAAATACAAACATTCTAAAATATTAATACA-AAAA-ATAAAAT
1 AAATTAAATTTACAAACACAA-AAAATACAAACATTCTAAAA-ATTAATACACAAAATATAAAAT
30794265 TCAAACAAAAATAATACGCACT
64 TCAAACAAAAATAATACGCACT
* * * *
30794287 AAATTAAATTTA-AACACCCAAAAAACTACAAACATATGGGT-AAAATTAATACACAAAAATTTT
1 AAATTAAATTTACAA-ACACAAAAAA-TACAAACAT-T--CTAAAAATTAATACAC-AAAATATA
* * *
30794350 AAATTCAAACTACATAA-AATATGGACT
60 AAATTCAAAC-A-AAAATAATACGCACT
*
30794377 AAATTAAATTTACAAATACAGAAAAATACAAACATTCTAAGAAATTAATACACGAAAATATAAAA
1 AAATTAAATTTACAAACACA-AAAAATACAAACATTCTAA-AAATTAATACAC-AAAATATAAAA
30794442 AATTAATCCT
Statistics
Matches: 127, Mismatches: 14, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
84 5 0.04
85 26 0.20
86 10 0.08
87 4 0.03
88 6 0.05
89 33 0.26
90 33 0.26
91 10 0.08
ACGTcount: A:0.58, C:0.13, G:0.04, T:0.24
Consensus pattern (85 bp):
AAATTAAATTTACAAACACAAAAAATACAAACATTCTAAAAATTAATACACAAAATATAAAATTC
AAACAAAAATAATACGCACT
Found at i:30794946 original size:27 final size:27
Alignment explanation
Indices: 30794908--30794973 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
30794898 TTCGATTGTA
* *
30794908 CACTACAAAAAACTCTCATCTACAATC
1 CACTACAAAAAACTCCCATATACAATC
30794935 CACTACAAAAAACTCCCATATACAATC
1 CACTACAAAAAACTCCCATATACAATC
30794962 CACTACAAAAAA
1 CACTACAAAAAA
30794974 AAACTCATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (27 bp):
CACTACAAAAAACTCCCATATACAATC
Found at i:30795242 original size:49 final size:46
Alignment explanation
Indices: 30795164--30795267 Score: 120
Period size: 49 Copynumber: 2.2 Consensus size: 46
30795154 GCCAGCAACG
* **
30795164 ATTTTTTTTTTACTCTGGTGTTAGTCAATA-AGTGCCCAACACTCAAA
1 ATTTTTTTTTTACTCTGGTGTCAACCAATATA-TGCCCAACAC-CAAA
* *
30795211 ATTTTTTTTTTCATTTCTGGTGTCAACCAATATATGCCCAACACCCAA
1 ATTTTTTTTTT-A-CTCTGGTGTCAACCAATATATGCCCAACACCAAA
30795259 ATTTTTTTT
1 ATTTTTTTT
30795268 AAAATTTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
47 11 0.22
48 13 0.27
49 24 0.49
50 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (46 bp):
ATTTTTTTTTTACTCTGGTGTCAACCAATATATGCCCAACACCAAA
Found at i:30795424 original size:113 final size:109
Alignment explanation
Indices: 30795276--30795609 Score: 341
Period size: 112 Copynumber: 3.0 Consensus size: 109
30795266 TTAAAATTTA
* *
30795276 ATGGTGCCAACCATCAGTGTAGAAAAGTAAGAAAAAAAATTACATTGGTACACGAAAAAAGTCTC
1 ATGGTGCCGACTATCAGTGTAGAAAAGTAA-AAAAAAAATTACATTGG-ACACGAAAAAAGTC-C
** *
30795341 TGGTGCTGGCCATTAGAAGGCCAGAACCAAAACTTTTTTTTTGTTGGT
63 TGGTGCTGGCCATTAGAAGGCCAGAACCAAAA-TTTTTTTTTACTAGT
* * * **
30795389 TTGGTGCCGACTATCAGTGTAAAAAAGTACAAAAAAAATTGTATTAGGACACGAAAAAAGTCCGT
1 ATGGTGCCGACTATCAGTGTAGAAAAGTAAAAAAAAAATTACATT-GGACACGAAAAAAGTCC-T
* ******
30795454 GGTG-TGGGCCATTAAAAGGCCAGAACCAAAAAAAAAATTTACTAGT
64 GGTGCT-GGCCATTAGAAGGCCAGAACCAAAATTTTTTTTTACTAGT
* * * *
30795500 ATGGTGTCGGCTATCAGTGTAGAAAAGTAAAAAAAAAAATTTACGGTGGGACACGAAAAAAGTCC
1 ATGGTGCCGACTATCAGTGTAGAAAAGT-AAAAAAAAAA-TTAC-ATTGGACACGAAAAAAGT-C
*
30795565 CTGGTGCCT-GCCATTAGAAGGCCAGAACC-AAATTTTTTTTAACTA
62 CTGGTG-CTGGCCATTAGAAGGCCAGAACCAAAATTTTTTTTTACTA
30795610 CTTGTATTTT
Statistics
Matches: 178, Mismatches: 34, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
111 32 0.18
112 74 0.42
113 68 0.38
114 3 0.02
115 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (109 bp):
ATGGTGCCGACTATCAGTGTAGAAAAGTAAAAAAAAAATTACATTGGACACGAAAAAAGTCCTGG
TGCTGGCCATTAGAAGGCCAGAACCAAAATTTTTTTTTACTAGT
Found at i:30797277 original size:21 final size:21
Alignment explanation
Indices: 30797253--30797301 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
30797243 GCTGCCATCA
* *
30797253 CTGCTGTCTCTACCTCCCTCG
1 CTGCTGCCGCTACCTCCCTCG
* *
30797274 CTGCTACCGCTGCCTCCCTCG
1 CTGCTGCCGCTACCTCCCTCG
30797295 CTGCTGC
1 CTGCTGC
30797302 ATCCACTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.49, G:0.18, T:0.29
Consensus pattern (21 bp):
CTGCTGCCGCTACCTCCCTCG
Found at i:30797740 original size:13 final size:14
Alignment explanation
Indices: 30797714--30797742 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
30797704 ACTAACGACG
30797714 AATTAAATCATTAT
1 AATTAAATCATTAT
30797728 AATTAAA-CATTAT
1 AATTAAATCATTAT
30797741 AA
1 AA
30797743 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTAAATCATTAT
Found at i:30804307 original size:11 final size:11
Alignment explanation
Indices: 30804293--30804337 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
30804283 AGATAAATAT
30804293 TATTTTATTAA
1 TATTTTATTAA
*
30804304 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
30804317 TATTTTATTAT
1 TATTTTATTAA
30804328 TATTTTATTA
1 TATTTTATTA
30804338 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:30806140 original size:46 final size:46
Alignment explanation
Indices: 30806088--30806548 Score: 552
Period size: 46 Copynumber: 10.0 Consensus size: 46
30806078 GTGTGCTTTC
*
30806088 TGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGAAATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
30806134 TGAAATGAAATGTGAAAGACTATGGTTGAAAGATACCATGGCAACA
1 TGAAATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
30806180 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGAAATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
30806226 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATTGCAACA
1 TGAAATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* *
30806272 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGAAATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
** * * * * *
30806318 T-AACGGGAAATGAATAAAACCATGGTTG-AAGATACCATGGTAGCG
1 TGAA-ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
30806363 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGAAATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
30806409 T-AACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGAA-ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * * *
30806455 TGACATGAAAAGAATAAAACCATAGTTGAAAGATTCCATGGCAACA
1 TGAAATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
30806501 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGAAATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
30806547 TG
1 TG
30806549 TCAAAGATAA
Statistics
Matches: 373, Mismatches: 36, Indels: 12
0.89 0.09 0.03
Matches are distributed among these distances:
45 39 0.10
46 333 0.89
47 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
TGAAATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:30806520 original size:229 final size:230
Alignment explanation
Indices: 30806106--30806543 Score: 603
Period size: 229 Copynumber: 1.9 Consensus size: 230
30806096 AATGTGTAAG
* *
30806106 ACCATGGTTGAAAGATACCATGGCAACATGAAATGAAATGTGAAAGACTATGGTTGAAAGATACC
1 ACCATGGTTGAAAGATACCATGGCAACATGAAATGAAATGTAAAAGACCATGGTTGAAAGATACC
* * * ** *
30806171 ATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAA
66 ATGGCAACATAACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAA
* ** * * * * * *
30806236 TGTGTAAGACCATGGTTGAAAGATACCATTGCAACATGATATGAAATGTGTAAGACCATGGTTGA
131 AGAATAAAACCATAGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATAGTTGA
*
30806301 AAGATACCATGGCAACATAACGGGAAATGAATAAA
196 AAGACACCATGGCAACATAACGGGAAATGAATAAA
* * * *
30806336 ACCATGGTTG-AAGATACCATGGTAGCGTGACATGAAATG-AATAAGACCATGGTTGAAAGATAC
1 ACCATGGTTGAAAGATACCATGGCAACATGAAATGAAATGTAA-AAGACCATGGTTGAAAGATAC
* *
30806399 CATGGCAACGTAACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAA
65 CATGGCAACATAACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAA
*
30806464 AAGAATAAAACCATAGTTGAAAGATTCCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTT
130 AAGAATAAAACCATAGTTGAAAGATACCATGGCAACATGACATG-AAATGAGTAAGACCATAGTT
*
30806528 GAAAGACACTATGGCA
194 GAAAGACACCATGGCA
30806544 TCATGTCAAA
Statistics
Matches: 180, Mismatches: 26, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
228 2 0.01
229 168 0.93
230 10 0.06
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (230 bp):
ACCATGGTTGAAAGATACCATGGCAACATGAAATGAAATGTAAAAGACCATGGTTGAAAGATACC
ATGGCAACATAACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAA
AGAATAAAACCATAGTTGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATAGTTGA
AAGACACCATGGCAACATAACGGGAAATGAATAAA
Found at i:30806849 original size:16 final size:17
Alignment explanation
Indices: 30806828--30806860 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30806818 ATGATGGAGC
30806828 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
30806844 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
30806861 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:30808047 original size:12 final size:12
Alignment explanation
Indices: 30808032--30808057 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30808022 ATCATCCTCT
30808032 TCATCAGATTCA
1 TCATCAGATTCA
30808044 TCATCAGATTCA
1 TCATCAGATTCA
30808056 TC
1 TC
30808058 CCTCGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:30809853 original size:9 final size:9
Alignment explanation
Indices: 30809775--30809905 Score: 74
Period size: 9 Copynumber: 14.7 Consensus size: 9
30809765 TAAGTATAAT
*
30809775 TAAGTTATA
1 TAAGTTATG
30809784 TAAGTTATG
1 TAAGTTATG
30809793 TAAGTTATG
1 TAAGTTATG
* * *
30809802 ATATGATATA
1 -TAAGTTATG
*
30809812 T-ATTTATG
1 TAAGTTATG
30809820 T-A-TTATG
1 TAAGTTATG
*
30809827 TAAGTTATA
1 TAAGTTATG
*
30809836 TAAATTATG
1 TAAGTTATG
30809845 TAAGTTATG
1 TAAGTTATG
* * *
30809854 AAATTTGATCTT
1 TAAGTT-A--TG
*
30809866 TAAATTATG
1 TAAGTTATG
30809875 TAAGTTATG
1 TAAGTTATG
30809884 T-A-TTATG
1 TAAGTTATG
*
30809891 TAAATTATG
1 TAAGTTATG
*
30809900 TGAGTT
1 TAAGTT
30809906 GCTGGTGAAC
Statistics
Matches: 93, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
7 12 0.13
8 8 0.09
9 60 0.65
10 7 0.08
11 1 0.01
12 5 0.05
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:30809890 original size:16 final size:16
Alignment explanation
Indices: 30809869--30809900 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30809859 TGATCTTTAA
*
30809869 ATTATGTAAGTTATGT
1 ATTATGTAAATTATGT
30809885 ATTATGTAAATTATGT
1 ATTATGTAAATTATGT
30809901 GAGTTGCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (16 bp):
ATTATGTAAATTATGT
Found at i:30812718 original size:15 final size:15
Alignment explanation
Indices: 30812695--30812726 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30812685 AAATAATAAT
30812695 TTATATATATTTATC
1 TTATATATATTTATC
*
30812710 TTATTTATATTTATC
1 TTATATATATTTATC
30812725 TT
1 TT
30812727 CTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATATATTTATC
Found at i:30815071 original size:22 final size:22
Alignment explanation
Indices: 30815045--30815104 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
30815035 AAAACCATGT
* * *
30815045 TATTTTTGTTGTTGTTTTTCCA
1 TATTTTTGCTATTATTTTTCCA
30815067 TA-TTTTGCTATTATTTTTCCA
1 TATTTTTGCTATTATTTTTCCA
* *
30815088 -ATTTTTGCCACTATTTT
1 TATTTTTGCTATTATTTT
30815105 GCTATAGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.91
22 2 0.06
ACGTcount: A:0.15, C:0.13, G:0.08, T:0.63
Consensus pattern (22 bp):
TATTTTTGCTATTATTTTTCCA
Found at i:30819129 original size:13 final size:13
Alignment explanation
Indices: 30819111--30819149 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
30819101 TTGAATGCCA
30819111 AGAAAATCAATAG
1 AGAAAATCAATAG
*
30819124 AGAAAATGAA-AG
1 AGAAAATCAATAG
30819136 AGATAAATCAATAG
1 AGA-AAATCAATAG
30819150 TATCTCCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 5 0.23
13 15 0.68
14 2 0.09
ACGTcount: A:0.62, C:0.05, G:0.18, T:0.15
Consensus pattern (13 bp):
AGAAAATCAATAG
Found at i:30823679 original size:47 final size:47
Alignment explanation
Indices: 30823628--30823718 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
30823618 CCTAAGAATA
* *
30823628 CTATCTATACTTAGTATTGGACAACGAAGAAAATCAGGGAGATCAAT
1 CTATCTATACTTAGTATCGGACAACGAAGAAAATCAGGAAGATCAAT
30823675 CTATCTATACTTAGTATCGGACAACGAAGAAAATCAGGAAGATC
1 CTATCTATACTTAGTATCGGACAACGAAGAAAATCAGGAAGATC
30823719 GAATTGCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (47 bp):
CTATCTATACTTAGTATCGGACAACGAAGAAAATCAGGAAGATCAAT
Found at i:30827573 original size:11 final size:11
Alignment explanation
Indices: 30827556--30827596 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
30827546 AAAAAAAATT
*
30827556 TTTTTTTTTTG
1 TTTTTTTGTTG
30827567 CTTTTTTTGTTG
1 -TTTTTTTGTTG
30827579 TTTTTTTGTTG
1 TTTTTTTGTTG
30827590 TTTTTTT
1 TTTTTTT
30827597 TTTTACTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTTG
Found at i:30827585 original size:14 final size:13
Alignment explanation
Indices: 30827554--30827600 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
30827544 CAAAAAAAAA
30827554 TTTTTTTTT-TTT
1 TTTTTTTTTGTTT
**
30827566 GCTTTTTTTGTTGT
1 TTTTTTTTTGTT-T
*
30827580 TTTTTTGTTGTTT
1 TTTTTTTTTGTTT
30827593 TTTTTTTT
1 TTTTTTTT
30827601 ACTATTTTGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
12 7 0.26
13 10 0.37
14 10 0.37
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:30829083 original size:13 final size:13
Alignment explanation
Indices: 30829065--30829089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30829055 TTTAAATGTG
30829065 AAATGAATATATT
1 AAATGAATATATT
30829078 AAATGAATATAT
1 AAATGAATATAT
30829090 AAAAGTTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAATGAATATATT
Found at i:30830169 original size:36 final size:36
Alignment explanation
Indices: 30830128--30830200 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
30830118 TATAGGCTAG
30830128 TTTTTATTTCAAATATTATATGTAAAATATTTCAAA
1 TTTTTATTTCAAATATTATATGTAAAATATTTCAAA
30830164 TTTTTATTTCAAATATTATATGTAAAATATTTCAAA
1 TTTTTATTTCAAATATTATATGTAAAATATTTCAAA
30830200 T
1 T
30830201 ATAATTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (36 bp):
TTTTTATTTCAAATATTATATGTAAAATATTTCAAA
Found at i:30832184 original size:2 final size:2
Alignment explanation
Indices: 30832177--30832249 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
30832167 CCTCCCTTCG
*
30832177 CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
30832219 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
30832250 CCCATGTATA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:30832287 original size:4 final size:4
Alignment explanation
Indices: 30832272--30832313 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
30832262 TTTCTTTGTG
*
30832272 TGTA TATA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
30832314 CATATATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:30833775 original size:2 final size:2
Alignment explanation
Indices: 30833768--30833807 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
30833758 ACAGGATTTG
30833768 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
30833808 TTATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:30836977 original size:11 final size:11
Alignment explanation
Indices: 30836963--30837003 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
30836953 TTTCAATATT
30836963 CTCTCAAATTC
1 CTCTCAAATTC
30836974 CTCTCAAA-TC
1 CTCTCAAATTC
*
30836984 TCTCTTAAATTC
1 -CTCTCAAATTC
30836996 CTCTCAAA
1 CTCTCAAA
30837004 ACTCTCGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 2 0.08
11 22 0.85
12 2 0.08
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:30837026 original size:22 final size:22
Alignment explanation
Indices: 30836962--30837017 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
30836952 CTTTCAATAT
* *
30836962 TCTCTCAAATTCCTCTCAAATC
1 TCTCTTAAATTCCTCTCAAAAC
30836984 TCTCTTAAATTCCTCTCAAAAC
1 TCTCTTAAATTCCTCTCAAAAC
30837006 TCTCGTTAAATT
1 TCTC-TTAAATT
30837018 TTTTCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.29, C:0.30, G:0.02, T:0.39
Consensus pattern (22 bp):
TCTCTTAAATTCCTCTCAAAAC
Found at i:30838733 original size:30 final size:30
Alignment explanation
Indices: 30838683--30838746 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
30838673 ACGACGCAGA
*
30838683 CCCATCAACAGCACCCACACAATCACCCGG
1 CCCAGCAACAGCACCCACACAATCACCCGG
* * * *
30838713 CCCAGCAACAGGACCTACACAGTCACCGGG
1 CCCAGCAACAGCACCCACACAATCACCCGG
30838743 CCCA
1 CCCA
30838747 ACAGTTCAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (30 bp):
CCCAGCAACAGCACCCACACAATCACCCGG
Found at i:30838823 original size:18 final size:18
Alignment explanation
Indices: 30838800--30838842 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
30838790 TGCCAGGTAC
*
30838800 GTATCCTAGCCCTTTTAT
1 GTATCCTAGCCCTTATAT
30838818 GTATCCTAGCCCTTATAT
1 GTATCCTAGCCCTTATAT
*
30838836 GTTTCCT
1 GTATCCT
30838843 TTTCCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (18 bp):
GTATCCTAGCCCTTATAT
Found at i:30839431 original size:116 final size:116
Alignment explanation
Indices: 30839227--30839493 Score: 480
Period size: 116 Copynumber: 2.3 Consensus size: 116
30839217 TATTTGTACA
* *
30839227 AACATTTTGAATCTTTATATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
* * * *
30839292 TGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGT
66 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
30839343 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
30839408 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
66 TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
30839459 AACATTTTGAATATTTTTATATTATTTCATGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAAT
30839494 AAAATATAAA
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 145 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.48
Consensus pattern (116 bp):
AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
TATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGC
Found at i:30839456 original size:54 final size:54
Alignment explanation
Indices: 30839276--30839457 Score: 181
Period size: 54 Copynumber: 3.2 Consensus size: 54
30839266 TAAAAGGTTG
* *
30839276 TTTTAAATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTA
1 TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
* * * * *
30839330 TTTTAAATAAGGTAACATTTTGAATATT--TTTATATTATTTCATGTAATTAGAT-AAAAGGTTG
1 TTTTAAATAAAGT-A-ATTAT-AAT-TTACTTT-TA-TATTT--T-TAATAAAATGAAAA--TTA
30839392 TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
1 TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
30839446 TTTTAAATAAAG
1 TTTTAAATAAAG
30839458 CAACATTTTG
Statistics
Matches: 103, Mismatches: 11, Indels: 28
0.73 0.08 0.20
Matches are distributed among these distances:
54 26 0.25
55 8 0.08
56 12 0.12
57 5 0.05
58 14 0.14
59 5 0.05
60 11 0.11
61 8 0.08
62 14 0.14
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (54 bp):
TTTTAAATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTA
Found at i:30842747 original size:126 final size:126
Alignment explanation
Indices: 30842509--30843046 Score: 830
Period size: 126 Copynumber: 4.3 Consensus size: 126
30842499 GCCCAAGTTA
* * *
30842509 TTTCAGAAACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGTTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*** *
30842574 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTATGCAGACATGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* * * * * *
30842635 TTTTAGAGACCACTGTAGTAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
30842700 TGCATCCTACTTGAAGCGTTTTT-ACCACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGA-CACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* *
30842761 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTACT-AACA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAA-A
* *
30842825 ATGCATCCTGCTTGAAGCGTTTTTTACACTATTTGCATAGACACGTCTTCTCAAAATTATTT
65 ATGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* * *
30842887 TTTCAAATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*
30842952 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAATTTA-TT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
30843012 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
30843047 AGAAGCTTTT
Statistics
Matches: 376, Mismatches: 32, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
125 38 0.10
126 336 0.89
127 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (126 bp):
TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
Found at i:30843259 original size:97 final size:96
Alignment explanation
Indices: 30843156--30843330 Score: 255
Period size: 97 Copynumber: 1.8 Consensus size: 96
30843146 CTTAAAATCC
* * **
30843156 TAATCTAATTTTTTTAAATTTA-TAATTAATTTACTTAAGTAAC-CTTAAACCCTAATTTATTTA
1 TAATCTAA-TTTTTTAAAATTAGTAATTAATTTAATTAACAAACAC-TAAACCCTAATTTATTTA
*
30843219 ATTTTTTTCTTTAAAAACCATAAACACTAAACCA
64 A-TTTTTTCCTTAAAAACCATAAACACTAAACCA
*
30843253 TAATCTAATTTTTTAAAATTAGTAATTAATTTAATTAACAAACACTAAACCTTAATTTATTTAAT
1 TAATCTAATTTTTTAAAATTAGTAATTAATTTAATTAACAAACACTAAACCCTAATTTATTTAAT
30843318 TTTTTCCTTAAAA
66 TTTTTCCTTAAAA
30843331 CCCTAAAATT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
96 25 0.36
97 44 0.63
98 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.45
Consensus pattern (96 bp):
TAATCTAATTTTTTAAAATTAGTAATTAATTTAATTAACAAACACTAAACCCTAATTTATTTAAT
TTTTTCCTTAAAAACCATAAACACTAAACCA
Found at i:30847575 original size:9 final size:9
Alignment explanation
Indices: 30847561--30847593 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
30847551 CTTATATTTT
30847561 TTTTTTTAC
1 TTTTTTTAC
30847570 TTTTTTTAAC
1 TTTTTTT-AC
30847580 -TTTTTTAC
1 TTTTTTTAC
30847588 TTTTTT
1 TTTTTT
30847594 CTTATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:30847678 original size:36 final size:36
Alignment explanation
Indices: 30847609--30847682 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 36
30847599 ATTTTGTCTC
*
30847609 TTTCTTAGATTTTTTTCTTTTTTAAGTTTTATATTAT
1 TTTCTTAGATTTTTTTCTTATTTAAG-TTTATATTAT
30847646 TTTCTTA-ATTTATTTTACTTATTTAA-TTTATATTAT
1 TTTCTTAGATTT-TTTT-CTTATTTAAGTTTATATTAT
30847682 T
1 T
30847683 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 15 0.44
37 11 0.32
38 8 0.24
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (36 bp):
TTTCTTAGATTTTTTTCTTATTTAAGTTTATATTAT
Found at i:30847687 original size:18 final size:17
Alignment explanation
Indices: 30847636--30847683 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
30847626 TTTTTTAAGT
*
30847636 TTTATATTATTTTCTTAA
1 TTTATATTATTAT-TTAA
*
30847654 TTTATTTTACTTATTTAA
1 TTTATATTA-TTATTTAA
30847672 TTTATATTATTA
1 TTTATATTATTA
30847684 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:30847696 original size:22 final size:22
Alignment explanation
Indices: 30847670--30847760 Score: 55
Period size: 22 Copynumber: 4.1 Consensus size: 22
30847660 TTACTTATTT
30847670 AATTTATATTATTAATTTTAAA
1 AATTTATATTATTAATTTTAAA
* *
30847692 AATTT-T-GTAATATATATTTAAA
1 AATTTATATTATTA-AT-TTTAAA
* *
30847714 ATGTTTTATAATATT--TTTTAAA
1 A--ATTTATATTATTAATTTTAAA
* * *
30847736 ATTTTAAATTATTATTTTTAAA
1 AATTTATATTATTAATTTTAAA
30847758 AAT
1 AAT
30847761 ATTCTTAACT
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
20 14 0.26
21 3 0.06
22 28 0.53
23 1 0.02
24 3 0.06
25 1 0.02
26 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATTTATATTATTAATTTTAAA
Found at i:30847720 original size:23 final size:22
Alignment explanation
Indices: 30847672--30847752 Score: 62
Period size: 23 Copynumber: 3.7 Consensus size: 22
30847662 ACTTATTTAA
*
30847672 TTTATATTATTAATTTTAAAA-AT
1 TTTATAATATT-A-TTTAAAATAT
* *
30847695 TTTGTAATATATATTTAAAATGT
1 TTTATAATAT-TATTTAAAATAT
*
30847718 TTTATAATATT-TTTTAAA-AT
1 TTTATAATATTATTTAAAATAT
30847738 TTTA-AATTATTATTT
1 TTTATAA-TATTATTT
30847753 TTAAAAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
19 2 0.04
20 9 0.19
21 9 0.19
22 8 0.17
23 19 0.40
24 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTATAATATTATTTAAAATAT
Found at i:30847759 original size:23 final size:21
Alignment explanation
Indices: 30847685--30847760 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 21
30847675 ATATTATTAA
*
30847685 TTTTAAAAATTTTGTAATATAT
1 TTTTAAAAATTTT-AAATATAT
* *
30847707 ATTTAAAATGTTTTATAATAT-T
1 TTTTAAAA-ATTTTA-AATATAT
30847729 TTTT-AAAATTTTAAATTATTAT
1 TTTTAAAAATTTTAAA-TA-TAT
30847751 TTTTAAAAAT
1 TTTTAAAAAT
30847761 ATTCTTAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.05
20 7 0.16
21 4 0.09
22 16 0.37
23 14 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTTAAAAATTTTAAATATAT
Found at i:30847842 original size:14 final size:15
Alignment explanation
Indices: 30847806--30847843 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
30847796 TATTTATAAA
*
30847806 TTTTAAAATTGTATT
1 TTTTAAAATTGAATT
30847821 TTTT-AAATT-AATT
1 TTTTAAAATTGAATT
30847834 TTTTAAAATT
1 TTTTAAAATT
30847844 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 7 0.33
14 10 0.48
15 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTTAAAATTGAATT
Found at i:30848548 original size:10 final size:9
Alignment explanation
Indices: 30848530--30848617 Score: 70
Period size: 9 Copynumber: 9.4 Consensus size: 9
30848520 TAAAATTTAA
30848530 AAAATATTT
1 AAAATATTT
30848539 AAAATCATTT
1 AAAAT-ATTT
*
30848549 AAAATATTA
1 AAAATATTT
30848558 AAAATATTT
1 AAAATATTT
*
30848567 TAAATCATTT
1 AAAAT-ATTT
* *
30848577 TAAATGTTTT
1 AAAAT-ATTT
* *
30848587 ATAATATTA
1 AAAATATTT
30848596 AAAATATATT
1 AAAATAT-TT
*
30848606 -TAATATTT
1 AAAATATTT
30848614 AAAA
1 AAAA
30848618 AATAATTTGA
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
8 2 0.03
9 35 0.56
10 25 0.40
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (9 bp):
AAAATATTT
Found at i:30848554 original size:19 final size:18
Alignment explanation
Indices: 30848530--30848617 Score: 70
Period size: 19 Copynumber: 4.7 Consensus size: 18
30848520 TAAAATTTAA
30848530 AAAATATTTAAAATCATTT
1 AAAATATTTAAAAT-ATTT
*
30848549 AAAATATTAAAAATATTT
1 AAAATATTTAAAATATTT
* * *
30848567 TAAATCATTTTAAATGTTTT
1 AAAAT-ATTTAAAAT-ATTT
* *
30848587 ATAATATTAAAAATATATT
1 AAAATATTTAAAATAT-TT
*
30848606 -TAATATTTAAAA
1 AAAATATTTAAAA
30848618 AATAATTTGA
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
18 20 0.36
19 29 0.53
20 6 0.11
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (18 bp):
AAAATATTTAAAATATTT
Found at i:30848640 original size:32 final size:33
Alignment explanation
Indices: 30848587--30848674 Score: 101
Period size: 32 Copynumber: 2.7 Consensus size: 33
30848577 TAAATGTTTT
30848587 ATAATATTAAAAATATATTTAATATTTA-AAAA
1 ATAATATTAAAAATATATTTAATATTTATAAAA
*
30848619 ATAAT-TTGAAAATATATTTTAATATTTATAAAA
1 ATAATATTAAAAATATA-TTTAATATTTATAAAA
* *
30848652 A-ATATATTATAAAACATTTTTAA
1 ATA-ATATTA-AAAATATATTTAA
30848675 AAAATACATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
31 10 0.21
32 17 0.36
33 7 0.15
34 7 0.15
35 6 0.13
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (33 bp):
ATAATATTAAAAATATATTTAATATTTATAAAA
Found at i:30848665 original size:13 final size:13
Alignment explanation
Indices: 30848639--30848680 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
30848629 AATATATTTT
30848639 AATATTTATAAAA
1 AATATTTATAAAA
30848652 AATATATTATAAAA
1 AATAT-TTATAAAA
*
30848666 CAT-TTT-TAAAA
1 AATATTTATAAAA
30848677 AATA
1 AATA
30848681 CATTTCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 7 0.28
12 2 0.08
13 6 0.24
14 10 0.40
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATTTATAAAA
Found at i:30852168 original size:30 final size:30
Alignment explanation
Indices: 30852134--30852236 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
30852124 CCTATATCCT
30852134 GGTGATATGAACTCGAACCACCCATGTCCG
1 GGTGATATGAACTCGAACCACCCATGTCCG
*
30852164 GGTGATATAAACTCGAACCACCCATGTCCG
1 GGTGATATGAACTCGAACCACCCATGTCCG
*
30852194 GGTGATATGAACTCGAACCACCTATGTCCG
1 GGTGATATGAACTCGAACCACCCATGTCCG
*
30852224 GGTTATATGAACT
1 GGTGATATGAACT
30852237 GCTCTGGGAC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (30 bp):
GGTGATATGAACTCGAACCACCCATGTCCG
Found at i:30855406 original size:22 final size:23
Alignment explanation
Indices: 30855381--30855431 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
30855371 ATATCTAATG
30855381 TTAAAAAAATTAAAAATA-ATAT
1 TTAAAAAAATTAAAAATATATAT
**
30855403 TT-AAAATTTTAAAAATATATAT
1 TTAAAAAAATTAAAAATATATAT
30855425 TATAAAA
1 T-TAAAA
30855432 TATTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 13 0.54
22 7 0.29
23 1 0.04
24 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAAAAAATTAAAAATATATAT
Found at i:30855408 original size:21 final size:23
Alignment explanation
Indices: 30855384--30855454 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
30855374 TCTAATGTTA
30855384 AAAAAATTAAAAATA-ATATT-T
1 AAAAAATTAAAAATATATATTAT
**
30855405 AAAATTTTAAAAATATATATTAT
1 AAAAAATTAAAAATATATATTAT
* ** * *
30855428 AAAATATTTTAAATATACATTAC
1 AAAAAATTAAAAATATATATTAT
30855451 AAAA
1 AAAA
30855455 TTTTTAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 13 0.32
22 5 0.12
23 23 0.56
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAAATTAAAAATATATATTAT
Found at i:30855441 original size:23 final size:22
Alignment explanation
Indices: 30855394--30855462 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 22
30855384 AAAAAATTAA
*
30855394 AAATA-ATATT-TAAAATTTTAA
1 AAATATATATTATAAAATTTT-T
30855415 AAATATATATTATAAAATATTTT
1 AAATATATATTATAAAAT-TTTT
* *
30855438 AAATATACATTACAAAATTTTT
1 AAATATATATTATAAAATTTTT
30855460 AAA
1 AAA
30855463 ATTAATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 5 0.12
22 12 0.29
23 22 0.52
24 3 0.07
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATATATATTATAAAATTTTT
Found at i:30855475 original size:21 final size:23
Alignment explanation
Indices: 30855404--30855476 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
30855394 AAATAATATT
* * *
30855404 TAAAATTTTAAAAATATATATTA
1 TAAAATTTTTAAAATATACATAA
*
30855427 TAAAATATTTT-AAATATACATTA
1 TAAAAT-TTTTAAAATATACATAA
*
30855450 CAAAATTTTTAAAAT-TA-ATAA
1 TAAAATTTTTAAAATATACATAA
30855471 TAAAAT
1 TAAAAT
30855477 AAATAAACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 8 0.19
22 6 0.14
23 26 0.60
24 3 0.07
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAATTTTTAAAATATACATAA
Found at i:30855479 original size:5 final size:5
Alignment explanation
Indices: 30855459--30855515 Score: 55
Period size: 5 Copynumber: 11.2 Consensus size: 5
30855449 ACAAAATTTT
*
30855459 TAAAA TTAATAA TAAAA T-AAA T-AAA CAAAA TAAAA TAAAA TAAGAA
1 TAAAA -TAA-AA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA
*
30855505 AAAAA TAAAA T
1 TAAAA TAAAA T
30855516 TTCAAAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
4 7 0.16
5 25 0.57
6 10 0.23
7 2 0.05
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:30855490 original size:21 final size:21
Alignment explanation
Indices: 30855466--30855515 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
30855456 TTTTAAAATT
*
30855466 AATAATAAAATAAAT-A-AAC
1 AATAATAAAATAAATAAGAAA
30855485 AA-AATAAAATAAAATAAGAAA
1 AATAATAAAAT-AAATAAGAAA
30855506 AA-AATAAAAT
1 AATAATAAAAT
30855516 TTCAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 8 0.30
19 6 0.22
20 1 0.04
21 12 0.44
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (21 bp):
AATAATAAAATAAATAAGAAA
Found at i:30855506 original size:18 final size:18
Alignment explanation
Indices: 30855469--30855515 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
30855459 TAAAATTAAT
30855469 AATAAAAT-AAATAAACAA
1 AATAAAATAAAATAAAC-A
*
30855487 AATAAAATAAAAT-AAGA
1 AATAAAATAAAATAAACA
30855504 AA-AAAATAAAAT
1 AATAAAATAAAAT
30855516 TTCAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 10 0.37
17 3 0.11
18 10 0.37
19 4 0.15
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (18 bp):
AATAAAATAAAATAAACA
Found at i:30855551 original size:36 final size:36
Alignment explanation
Indices: 30855485--30855560 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
30855475 ATAAATAAAC
*
30855485 AAAATAAAATAAAATAAGAAAAAAATAAAATTTCAA
1 AAAATAAAATAAAATAAGAAAAAAACAAAATTTCAA
* *
30855521 AAAAGTAAAA-AAAA-AAGGAAAAAGACAAAATTTTAA
1 AAAA-TAAAATAAAATAA-GAAAAAAACAAAATTTCAA
30855557 AAAA
1 AAAA
30855561 ATATTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 2 0.06
36 28 0.80
37 5 0.14
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.16
Consensus pattern (36 bp):
AAAATAAAATAAAATAAGAAAAAAACAAAATTTCAA
Found at i:30855592 original size:27 final size:28
Alignment explanation
Indices: 30855562--30855625 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
30855552 TTTAAAAAAA
* * *
30855562 TATTTAAAATATTATGATTTCTTATAT-
1 TATTTAAAAAATTATAATTTCTTAAATG
*
30855589 TA-TTAAAAAATTATAATTTTTTAAATG
1 TATTTAAAAAATTATAATTTCTTAAATG
30855616 TATTTAAAAA
1 TATTTAAAAA
30855626 TTGTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 20 0.65
27 4 0.13
28 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (28 bp):
TATTTAAAAAATTATAATTTCTTAAATG
Found at i:30855633 original size:26 final size:26
Alignment explanation
Indices: 30855562--30855627 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
30855552 TTTAAAAAAA
* *
30855562 TATTTAAAATATTATGATTTCTTATAT
1 TATTTAAAA-ATTATAATTTCTTAAAT
* *
30855589 TATTAAAAAATTATAATTTTTTAAAT
1 TATTTAAAAATTATAATTTCTTAAAT
30855615 GTATTTAAAAATT
1 -TATTTAAAAATT
30855628 GTATTTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (26 bp):
TATTTAAAAATTATAATTTCTTAAAT
Found at i:30855803 original size:20 final size:21
Alignment explanation
Indices: 30855778--30855816 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
30855768 AAAAAAGAAA
30855778 AAAAT-ATATTTAATATTTAT
1 AAAATAATATTTAATATTTAT
30855798 AAAATAATATTTAATATTT
1 AAAATAATATTTAATATTT
30855817 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATAATATTTAATATTTAT
Found at i:30855840 original size:18 final size:17
Alignment explanation
Indices: 30855806--30855847 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
30855796 ATAAAATAAT
*
30855806 ATTTAATATTTTTTTTAA
1 ATTT-ATATTTTATTTAA
30855824 ATTTATATTTATATTTAA
1 ATTTATATTT-TATTTAA
30855842 ATTTAT
1 ATTTAT
30855848 TAATAGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATATTTTATTTAA
Found at i:30856154 original size:22 final size:21
Alignment explanation
Indices: 30856102--30856188 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
30856092 TAAAGTTAAA
30856102 AAAATATTTTTAAAAATAATAAT
1 AAAA-ATTTTTAAAAAT-ATAAT
* *
30856125 TAAAATTTTTAAAAATATTAT
1 AAAAATTTTTAAAAATATAAT
* *
30856146 AAAACA-TTTTAAATATATATT
1 AAAA-ATTTTTAAAAATATAAT
** *
30856167 ACCAATTTTTTAAAAT-TAAT
1 AAAAATTTTTAAAAATATAAT
30856187 AA
1 AA
30856189 TATAAATTAA
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
20 5 0.10
21 29 0.58
22 13 0.26
23 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAAATTTTTAAAAATATAAT
Found at i:30856196 original size:23 final size:23
Alignment explanation
Indices: 30856103--30856196 Score: 70
Period size: 22 Copynumber: 4.2 Consensus size: 23
30856093 AAAGTTAAAA
30856103 AAATATTTTTAAAAATAATAAT-T
1 AAAT-TTTTTAAAAATAATAATAT
* *
30856126 AAAATTTTTAAAAAT-ATTATA-
1 AAATTTTTTAAAAATAATAATAT
** * * *
30856147 AAACATTTTAAATAT-ATATTAC
1 AAATTTTTTAAAAATAATAATAT
* *
30856169 CAATTTTTTAAAATTAATAATAT
1 AAATTTTTTAAAAATAATAATAT
30856192 AAATT
1 AAATT
30856197 AAATAAGTAA
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
21 20 0.38
22 21 0.40
23 12 0.23
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTTTTTAAAAATAATAATAT
Found at i:30856229 original size:18 final size:18
Alignment explanation
Indices: 30856179--30856230 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
30856169 CAATTTTTTA
*
30856179 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
* *
30856197 AAATAAGTAAAATAAATT
1 AAATAAATAATATAAATT
30856215 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
30856231 ACTTAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:30856281 original size:9 final size:9
Alignment explanation
Indices: 30856267--30856308 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
30856257 AAAATATAAG
30856267 AAAAAAAGT
1 AAAAAAAGT
30856276 -AAAAAAGT
1 AAAAAAAGT
30856284 AAAAAAAGT
1 AAAAAAAGT
*
30856293 AAGAAAAGT
1 AAAAAAAGT
30856302 AAAAAAA
1 AAAAAAA
30856309 AAATATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:30856289 original size:17 final size:18
Alignment explanation
Indices: 30856267--30856308 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
30856257 AAAATATAAG
30856267 AAAAAAAGTAA-AAAAGT
1 AAAAAAAGTAAGAAAAGT
30856284 AAAAAAAGTAAGAAAAGT
1 AAAAAAAGTAAGAAAAGT
30856302 AAAAAAA
1 AAAAAAA
30856309 AAATATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAAAAAGTAAGAAAAGT
Found at i:30858757 original size:27 final size:28
Alignment explanation
Indices: 30858727--30858788 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
30858717 TATAAAAGGT
* *
30858727 TTAAATTGA-TTTATAATTTTTAAAGAA
1 TTAAATTAATTTTATAATTTTTAAAAAA
*
30858754 TTAAATTAATTTTTTATTATTTTTAAAAAA
1 TTAAATTAA--TTTTATAATTTTTAAAAAA
30858784 TTAAA
1 TTAAA
30858789 GTAAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 8 0.28
30 21 0.72
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
TTAAATTAATTTTATAATTTTTAAAAAA
Found at i:30858757 original size:109 final size:110
Alignment explanation
Indices: 30858635--30858843 Score: 296
Period size: 110 Copynumber: 1.9 Consensus size: 110
30858625 TCTTCATAGA
* *
30858635 TTTTAAATGATTAAATAAAATTTTTATCATTTTT-AAAAGCTAAAGTACAATTTTACCATTACTA
1 TTTTAAATGATTAAATAAAATTTTTATCATTTTTAAAAAACTAAAGTAAAATTTTACCATTACTA
* *
30858699 ATTTAAAGTTTTATAAATTATAAAAGGTTTAAATTGATTTATAAT
66 AATTAAAATTTTATAAATTATAAAAGGTTTAAATTGATTTATAAT
* * * * **
30858744 TTTTAAA-GAATTAAATTAATTTTTTATTATTTTTAAAAAATTAAAGTAAAATTTTATTATTACT
1 TTTTAAATG-ATTAAATAAAATTTTTATCATTTTTAAAAAACTAAAGTAAAATTTTACCATTACT
*
30858808 AAATTAAAATTTTATAAATTGTAAAAGGTTTAAATT
65 AAATTAAAATTTTATAAATTATAAAAGGTTTAAATT
30858844 ACAATTTTAA
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
108 1 0.01
109 29 0.33
110 57 0.66
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (110 bp):
TTTTAAATGATTAAATAAAATTTTTATCATTTTTAAAAAACTAAAGTAAAATTTTACCATTACTA
AATTAAAATTTTATAAATTATAAAAGGTTTAAATTGATTTATAAT
Found at i:30858776 original size:30 final size:30
Alignment explanation
Indices: 30858736--30858804 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
30858726 TTTAAATTGA
* * * **
30858736 TTTATAATTTTTAAAGAATTAAATTAATTT
1 TTTATTATTTTTAAAAAATTAAAGTAAAAT
30858766 TTTATTATTTTTAAAAAATTAAAGTAAAAT
1 TTTATTATTTTTAAAAAATTAAAGTAAAAT
30858796 TTTATTATT
1 TTTATTATT
30858805 ACTAAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TTTATTATTTTTAAAAAATTAAAGTAAAAT
Found at i:30859220 original size:13 final size:13
Alignment explanation
Indices: 30859202--30859232 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30859192 GTATAAATGT
*
30859202 ATATTGAATATAA
1 ATATTGAATAAAA
30859215 ATATTGAATAAAA
1 ATATTGAATAAAA
30859228 ATATT
1 ATATT
30859233 TAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (13 bp):
ATATTGAATAAAA
Found at i:30869492 original size:30 final size:30
Alignment explanation
Indices: 30869456--30869517 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
30869446 TACCATTGAA
*
30869456 GAATAAATCTCCAATAGTTCACTTTATATC
1 GAATAAATCTCCAACAGTTCACTTTATATC
30869486 GAATAAATCTCCAACAGTTCACTTTATATC
1 GAATAAATCTCCAACAGTTCACTTTATATC
30869516 GA
1 GA
30869518 TCTTTATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (30 bp):
GAATAAATCTCCAACAGTTCACTTTATATC
Found at i:30875268 original size:3 final size:3
Alignment explanation
Indices: 30875260--30875294 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
30875250 GGTTTAAATA
*
30875260 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
30875295 GATTTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:30881173 original size:22 final size:22
Alignment explanation
Indices: 30881148--30881193 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
30881138 AACTTATCTT
30881148 ACCTTTTAAACAACTCTAAACC
1 ACCTTTTAAACAACTCTAAACC
30881170 ACCTTTTAAACAACTCTAAACC
1 ACCTTTTAAACAACTCTAAACC
30881192 AC
1 AC
30881194 TTATTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (22 bp):
ACCTTTTAAACAACTCTAAACC
Found at i:30882413 original size:44 final size:45
Alignment explanation
Indices: 30882360--30882462 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 45
30882350 TGTCTTTGAC
* * * * *
30882360 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCATATCTCCAAAGCCATATTATAAT
** *
30882404 ATGGACTTACATGGCTCAATCATATCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCATATCTCCAAAGCCATA-TTATAAT
30882450 ATGGACTTACATG
1 ATGGACTTACATG
30882463 GCTCATTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 31 0.63
46 18 0.37
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCATATCTCCAAAGCCATATTATAAT
Found at i:30889846 original size:46 final size:44
Alignment explanation
Indices: 30889742--30889849 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
30889732 TGTCTTTGAC
** * * *
30889742 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
30889786 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
30889832 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
30889850 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:30899521 original size:3 final size:3
Alignment explanation
Indices: 30899513--30899543 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30899503 AGAAAAGGCT
30899513 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
30899544 GATGGCTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:30902485 original size:23 final size:23
Alignment explanation
Indices: 30902459--30902502 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
30902449 ATACACGAAT
30902459 TCCAACCAAACACACCAGAATAA
1 TCCAACCAAACACACCAGAATAA
*
30902482 TCCACCCAAACACACCAGAAT
1 TCCAACCAAACACACCAGAAT
30902503 GGCACTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.39, G:0.05, T:0.09
Consensus pattern (23 bp):
TCCAACCAAACACACCAGAATAA
Found at i:30903145 original size:16 final size:16
Alignment explanation
Indices: 30903124--30903155 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
30903114 TAATGTGTTT
30903124 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
30903140 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
30903156 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:30903337 original size:45 final size:45
Alignment explanation
Indices: 30903269--30903487 Score: 339
Period size: 45 Copynumber: 4.9 Consensus size: 45
30903259 AAGAGGTGAA
** * * *
30903269 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
30903314 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
30903359 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* *
30903404 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* * * *
30903449 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCA
30903488 CCATGGCCGA
Statistics
Matches: 162, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 162 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:30905189 original size:26 final size:26
Alignment explanation
Indices: 30905154--30905203 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
30905144 AAATAAAAAG
*
30905154 GGGGTTGCTATGTGCTGATTCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCAA
30905180 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
30905204 GATTAAGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.24, G:0.32, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:30905223 original size:102 final size:104
Alignment explanation
Indices: 30904972--30905236 Score: 410
Period size: 104 Copynumber: 2.6 Consensus size: 104
30904962 GTTGTACATA
** *
30904972 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
30905037 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
30905076 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
30905140 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATT-CCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
30905178 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
30905237 AATAACGGTT
Statistics
Matches: 148, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
102 57 0.39
103 26 0.18
104 65 0.44
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:30906882 original size:69 final size:69
Alignment explanation
Indices: 30906800--30906934 Score: 270
Period size: 69 Copynumber: 2.0 Consensus size: 69
30906790 ATGGTTTTGT
30906800 AAAAAAAAAAATTTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAA
1 AAAAAAAAAAATTTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAA
30906865 ATCA
66 ATCA
30906869 AAAAAAAAAAATTTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAA
1 AAAAAAAAAAATTTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAA
30906934 A
66 A
30906935 AAAGAGTCTG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.48, C:0.16, G:0.21, T:0.16
Consensus pattern (69 bp):
AAAAAAAAAAATTTTGCCTACGGTCTAGGCGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAA
ATCA
Found at i:30909856 original size:16 final size:16
Alignment explanation
Indices: 30909835--30909866 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
30909825 TAATGTGTTT
30909835 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
30909851 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
30909867 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:30910048 original size:45 final size:45
Alignment explanation
Indices: 30909980--30910153 Score: 249
Period size: 45 Copynumber: 3.9 Consensus size: 45
30909970 AAGAGGTGAA
**
30909980 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
* * *
30910025 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
* * *
30910070 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
* * *
30910115 CAACATCATGCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCA
30910154 CCATGGCCGA
Statistics
Matches: 117, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 117 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
Found at i:30911060 original size:16 final size:15
Alignment explanation
Indices: 30911034--30911073 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
30911024 TCACTCTCTA
30911034 TTTCTTTTTATGCTTT
1 TTTC-TTTTATGCTTT
*
30911050 GTTTCTTTTATTCTTT
1 -TTTCTTTTATGCTTT
30911066 TTTCTTTT
1 TTTCTTTT
30911074 CTTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 10 0.45
17 4 0.18
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (15 bp):
TTTCTTTTATGCTTT
Found at i:30913919 original size:47 final size:47
Alignment explanation
Indices: 30913810--30913920 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
30913800 CCGGGATAAG
* *
30913810 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
30913857 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
30913904 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
30913921 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:30914688 original size:4 final size:4
Alignment explanation
Indices: 30914679--30914703 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
30914669 CCCTTTTCTA
30914679 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
30914704 CACGATTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:30919601 original size:18 final size:17
Alignment explanation
Indices: 30919573--30919607 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30919563 ATTATTAAGA
*
30919573 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
30919590 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
30919608 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:30919835 original size:44 final size:45
Alignment explanation
Indices: 30919767--30919861 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
30919757 TTACACCTCT
*
30919767 ATTACATTCAACCAAACACATGA-TTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACATGATTTACTATTACACCTCTATTCC
** *
30919811 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACATGATTTACTATTACACCTCTATTCC
30919856 ATTACA
1 ATTACA
30919862 CCTCTATTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 21 0.46
45 25 0.54
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (45 bp):
ATTACATTCAACCAAACACATGATTTACTATTACACCTCTATTCC
Found at i:30919861 original size:16 final size:16
Alignment explanation
Indices: 30919840--30919909 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
30919830 TTGATTTGCT
*
30919840 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
30919856 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
30919872 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
30919888 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
30919904 AATACA
1 ATTACA
30919910 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:30920052 original size:19 final size:20
Alignment explanation
Indices: 30920012--30920053 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
30920002 AAATTTAAAA
*
30920012 TTAAGAATTAAATATTTTTT
1 TTAAGAATTAAATATTTATT
30920032 TTAA-AATT-AATATTTAATT
1 TTAAGAATTAAATATTT-ATT
30920051 TTA
1 TTA
30920054 TCAAACAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 7 0.35
19 9 0.45
20 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTAAGAATTAAATATTTATT
Found at i:30943572 original size:47 final size:46
Alignment explanation
Indices: 30943516--30943731 Score: 249
Period size: 47 Copynumber: 4.5 Consensus size: 46
30943506 GTGTGCTCTT
*
30943516 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCC
1 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
30943562 TGATAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGAT-ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
30943609 TGATATGAAATGTGTAAAGACCATGGTTGAATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGTGT-AAGACC--------ATGGTTGAAAGATACCATGGCAACC
* *
30943664 TGATATGAAATG-GAACAGACCAT-GTTGAAAGATACCATGGCAACA
1 TGATATGAAATGTGTA-AGACCATGGTTGAAAGATACCATGGCAACC
* *
30943709 TGACA-GAAAATGAGTAAGACCAT
1 TGATATG-AAATGTGTAAGACCAT
30943732 AGTGAAGACA
Statistics
Matches: 151, Mismatches: 6, Indels: 27
0.82 0.03 0.15
Matches are distributed among these distances:
44 1 0.01
45 37 0.25
46 19 0.13
47 51 0.34
53 1 0.01
54 6 0.04
55 36 0.24
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (46 bp):
TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
Found at i:30943668 original size:55 final size:53
Alignment explanation
Indices: 30943584--30943692 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 53
30943574 GTGTAAGACC
30943584 ATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAA-AGACCATGGTTGA
1 ATGGTTGAAAGATACCATGGCAACCTGATATGAAATG-G-AACAGACCAT-GTTGA
*
30943639 ATGGTTGAAAGATACCATGGCAACGTGATATGAAATGGAACAGACCATGTTGA
1 ATGGTTGAAAGATACCATGGCAACCTGATATGAAATGGAACAGACCATGTTGA
30943692 A
1 A
30943693 AGATACCATG
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
53 8 0.15
54 8 0.15
55 36 0.69
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.24
Consensus pattern (53 bp):
ATGGTTGAAAGATACCATGGCAACCTGATATGAAATGGAACAGACCATGTTGA
Found at i:30944842 original size:12 final size:12
Alignment explanation
Indices: 30944804--30944850 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
30944794 AAACTTAAAC
30944804 AAATAAATAAG-
1 AAATAAATAAGT
30944815 AAAGTGAAATAAGT
1 AAA-T-AAATAAGT
*
30944829 AAATAAATAGGT
1 AAATAAATAAGT
30944841 AAATAAATAA
1 AAATAAATAA
30944851 AATATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 3 0.10
12 17 0.55
13 8 0.26
14 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (12 bp):
AAATAAATAAGT
Done.